The one has nothing to do with the other. I use VLC and Handbrake on all of my Macs. Handbrake is 64-bit and I can't remember which VLC I am using. I just download it from the VLC website.
I must tell you that I've been using Handbrake and VLC for 2 years now, have ripped about 4 TB of my DVDs and BRs and have never seen that. I've also never really paid attention to which versions I was installing. I totally misunderstood your first post.
I just checked to make sure and I am currently using the 64 bit Handbrake and 64 bit VLC. Is there any particular reason why you don't want to install 64-bit VLC?
Handbrake has auto update. I don't remember if VLC does auto update, but it does have a Check For Update button in the application meu. I just remember to hit it once a month.
I use iDentify. It's a great little app which downloads the artwork and writes the correct info into the m4v/mpg file so that it shows up in iTunes under the correct place (TV series or Movies) and with the artwork, season number, description and so forth. You just have to make sure that you name your output files from Handbrake in the format that iDentify can understand.